diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 123 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 21 | ||||
| -rw-r--r-- | gn/packages/python.scm | 2 |
3 files changed, 115 insertions, 31 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 295a2b3..5bf7843 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -100,10 +100,11 @@ mappability data (files created by GEM). ") (license license:gpl2+))) (define-public freebayes - (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")) + (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb") + (revision "1")) (package (name "freebayes") - (version (string-append "v1.0.2-" (string-take commit 7))) + (version (string-append "1.0.2-" revision "." (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference @@ -113,11 +114,18 @@ mappability data (files created by GEM). ") (sha256 (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib))) (native-inputs - `(("cmake" ,cmake) + `(("bc" ,bc) ; Needed for running tests. + ("samtools" ,samtools) ; Needed for running tests. + ("parallel" ,parallel) ; Needed for running tests. + ("procps" ,procps) ; Needed for running tests. + ("bamtools" ,bamtools) + ("cmake" ,cmake) ("htslib" ,htslib) - ("zlib" ,zlib) ("python" ,python-2) + ("r" ,r) ("perl" ,perl) ("bamtools-src" ,(origin @@ -193,20 +201,34 @@ mappability data (files created by GEM). ") (file-name "fastahack-src.tar.gz") (sha256 (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2")))) - )) + ;; These submodules are needed to run the tests. + ("bash-tap-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/illusori/bash-tap/archive/" + "c38fbfa401600cc81ccda66bfc0da3ea56288d03" ".tar.gz")) + (file-name "bash-tap-src.tar.gz") + (sha256 + (base32 "07ijb1p0aa65ajpg9nkghc183iha6lwiydkckay8pghapa01j6nz")))) + ("test-simple-bash-src" + ,(origin + (method url-fetch) + (uri (string-append "https://github.com/ingydotnet/test-simple-bash/archive/" + "124673ff204b01c8e96b7fc9f9b32ee35d898acc" ".tar.gz")) + (file-name "test-simple-bash-src.tar.gz") + (sha256 + (base32 "016xf3wbgqbav9dncvfdx5k0f10z5xwq8jdszajzmcvnhz5wis14")))))) (arguments - `(#:tests? #f - #:phases + `(#:phases (modify-phases %standard-phases (delete 'configure) - (delete 'check) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs #:allow-other-keys) (let ((unpack (lambda (source target) (with-directory-excursion target (zero? (system* "tar" "xvf" - (assoc-ref inputs source) - "--strip-components=1")))))) + (assoc-ref inputs source) + "--strip-components=1")))))) (and (unpack "bamtools-src" "bamtools") (unpack "vcflib-src" "vcflib") @@ -217,47 +239,46 @@ mappability data (files created by GEM). ") (unpack "intervaltree-src" "vcflib/intervaltree") (unpack "multichoose-src" "vcflib/multichoose") (unpack "smithwaterman-src" "vcflib/smithwaterman") - (unpack "tabixpp-src" "vcflib/tabixpp"))))) + (unpack "tabixpp-src" "vcflib/tabixpp") + (unpack "test-simple-bash-src" "test/test-simple-bash") + (unpack "bash-tap-src" "test/bash-tap"))))) (add-after 'unpack-submodule-sources 'fix-makefile (lambda* (#:key inputs #:allow-other-keys) + ;; We don't have the .git folder to get the version tag from. + ;; For this checkout of the code, it's v1.0.0. (substitute* '("vcflib/Makefile") (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0")))) - (replace - 'build + (replace 'build (lambda* (#:key inputs make-flags #:allow-other-keys) (and - ;; We must compile Bamtools before we can compile the main - ;; project. + ;; Compile Bamtools before compiling the main project. (with-directory-excursion "bamtools" (system* "mkdir" "build") (with-directory-excursion "build" (and (zero? (system* "cmake" "../")) (zero? (system* "make"))))) - ;; We must compile vcflib before we can compile the main - ;; project. + ;; Compile vcflib before we compiling the main project. (with-directory-excursion "vcflib" (with-directory-excursion "tabixpp" (zero? (system* "make"))) (zero? (system* "make" "CC=gcc" (string-append "CFLAGS=\"" "-Itabixpp " "-I" (assoc-ref inputs "htslib") "/include " "\"") "all"))) - (with-directory-excursion "src" (zero? (system* "make")))))) - (replace - 'install + (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (install-file "bin/freebayes" bin) (install-file "bin/bamleftalign" bin)))) - ;; (replace - ;; 'check - ;; (lambda* (#:key outputs #:allow-other-keys) - ;; (with-directory-excursion "test" - ;; (zero? (system* "make" "test"))))) - ))) + ;; There are three tests that fail. All because of the -P + ;; (--perl-regexp) option in grep, which is not compiled into the + ;; version of grep in Guix. + (replace 'check + (lambda* (#:key inputs #:allow-other-keys) + (system* "make" "test")))))) (home-page "https://github.com/ekg/freebayes") - (synopsis "haplotype-based variant detector.") + (synopsis "Haplotype-based variant detector") (description "FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and @@ -305,8 +326,8 @@ length of a short-read sequencing alignment.") (propagated-inputs `( ;; ("r-annotationdbi" ,r-annotationdbi) ; ("r-biocparallel" ,r-biocparallel) - ("r-dynamictreecut" ,r-dynamictreecut) ("r-doparallel" ,r-doparallel) + ("r-dynamictreecut" ,r-dynamictreecut) ("r-fastcluster" ,r-fastcluster) ("r-foreach" ,r-foreach) ("r-go-db" ,r-go-db) @@ -793,3 +814,49 @@ format, and a collection of command-line utilities for executing complex manipulations on VCF files.") (license license:expat)))) +(define-public pindel + (package + (name "pindel") + (version "0.2.5b8") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/genome/pindel/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "06bsf0psxwf7h5p3j97xkh9k5qrwhxh6xn942y1j1m2inyhgs8bz")))) + (build-system gnu-build-system) + (inputs + `(("samtools" ,samtools) + ("htslib" ,htslib) + ("zlib" ,zlib))) + (native-inputs + `(("cppcheck" ,cppcheck) + ("python" ,python-2) + ("perl" ,perl))) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + ;; The first run creates a Makefile.local file. + (system* "make" (string-append "SAMTOOLS=" (assoc-ref inputs "samtools"))) + ;; The second run actually compiles the program. + (zero? (system* "make")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "src/pindel" bin) + (install-file "src/pindel2vcf" bin) + (install-file "src/pindel2vcf4tcga" bin) + (install-file "src/sam2pindel" bin))))))) + (home-page "https://github.com/genome/pindel") + (synopsis "Structural variants detector for next-gen sequencing data") + (description "Pindel can detect breakpoints of large deletions, medium sized +insertions, inversions, tandem duplications and other structural variants at +single-based resolution from next-gen sequence data. It uses a pattern growth +approach to identify the breakpoints of these variants from paired-end short +reads.") + (license license:gpl3+))) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index fdcbb7f..3d62d55 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -154,10 +154,14 @@ (sha256 (base32 "1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618")))) + (inputs `( + ("r-wgcna" ,r-wgcna) + ("r-qtl" ,r-qtl))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) ("r-wgcna" ,r-wgcna) + ("r-qtl" ,r-qtl) ("redis" ,redis) ("mysql" ,mysql) ("gemma" ,gemma-git) @@ -181,6 +185,7 @@ ("python2-passlib" ,python2-passlib) ("python2-piddle-gn" ,python2-piddle-gn) ("python2-redis" ,python2-redis) + ("python2-pil" ,python2-pil) ("python2-requests" ,python2-requests) ("python2-rpy2" ,python2-rpy2) ("python2-scipy" ,python2-scipy) @@ -190,7 +195,6 @@ ;; python-yolk is not needed ("plink" ,plink) ("qtlreaper" ,qtlreaper) - ("r-qtl" ,r-qtl) )) (build-system python-build-system) (arguments @@ -199,9 +203,20 @@ (modify-phases %standard-phases (add-before 'install 'fix-paths (lambda* (#:key inputs #:allow-other-keys) - (let* ((datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" ))) + (let* ( + (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" )) + (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) + (plink2cmd (string-append (assoc-ref inputs "plink2") "/bin/plink2")) + (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) + ) + (substitute* '("etc/default_settings.py") - (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))))))) + (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) + (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) + (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) + (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) + ) + )))) #:tests? #f)) ; no 'setup.py test' (home-page "http://genenetwork.org/") (synopsis "Full genenetwork services") diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 6fff9a3..8157c0b 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -432,6 +432,8 @@ version ".tgz")) (build-system python-build-system) (native-inputs `(("python2-setuptools" ,python2-setuptools))) + (propagated-inputs + `(("python2-pil" ,python2-pil))) (arguments `( #:python ,python-2 |